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Author Rice, Stuart A
Title Advances in Chemical Physics
Imprint Somerset : John Wiley & Sons, Incorporated, 2014
book jacket
Edition 1st ed
Descript 1 online resource (298 pages)
text txt rdacontent
computer c rdamedia
online resource cr rdacarrier
Series Advances in Chemical Physics Ser
Advances in Chemical Physics Ser
Note Advances in Chemical Physics -- Contributors to Volume 155 -- Preface to The Series -- Contents -- Modeling Viral Capsid Assembly -- I. Introduction -- A. Virus Anatomies -- B. Virus Assembly -- 1. Experiments That Characterize Capsid Assembly -- 2. Motivation for and Scope of Modeling -- II. Thermodynamics of Capsid Assembly -- A. Driving Forces -- B. Law of Mass Action -- 1. Estimating Binding Energies from Experiments -- III. Modeling Self-Assembly Dynamics and Kinetics of Empty Capsids -- A. Timescales for Capsid Assembly -- 1. Scaling Estimates for Assembly Timescales -- 2. Lag Times -- 3. The Slow Approach to Equilibrium -- B. Rate Equation Models for Capsid Assembly -- C. Particle-Based Simulations of Capsid Assembly Dynamics -- D. Conclusions from Assembly Dynamics Models -- E. Differences Among Models -- F. Higher T Numbers -- 1. Structural Stability of Different Capsid Geometries -- 2. Dynamics of Forming Icosahedral Geometries -- IV. Cargo-Containing Capsids -- A. Structures -- B. The Thermodynamics of Core-Controlled Assembly -- C. Single-Stranded RNA Encapsidation -- D. Dynamics of Assembly Around Cores -- V. Outlook -- References -- Charges at Aqueous Interfaces: Development of Computational Approaches in Direct Contact With Experiment -- I. Introduction -- II. Accounting for Polarizability Effects -- A. Models with Explicit Polarization -- B. Implicit Polarization via Charge Scaling -- C. Beyond Conventional Force Fields -- III. Case Studies -- A. Hydroxide at Aqueous Interfaces -- B. Solvated Electron at the Surface of Water -- IV. Outlook -- References -- Solute Precipitate Nucleation: A Review of Theory and Simulation Advances -- I. Introduction -- II. Classical Nucleation Theory -- A. Homogeneous Nucleation -- B. Heterogeneous Nucleation -- C. Nucleation Theorem -- III. Two-Step Nucleation Theory
A. Metastable Fluid--Fluid Critical Points -- B. Phenomenological Theories -- C. Coupled Flux Theories and Concentration Fluctuation Gating -- IV. Simulation Challenges -- A. Landau Free Energies and Rare Events -- B. Kramers--Langer--Berezhkovskii--Szabo (KLBS) Theory -- C. Nucleus Size in Simulations -- D. Which Nucleus Size Metric? -- E. Open versus Closed Systems -- V. Case Studies -- A. Laser-Induced Nucleation -- B. Nucleation of Methane Hydrates -- C. Nucleation of Calcium Carbonate -- VI. Closing Remarks -- References -- Water in The Liquid State: A Computational Viewpoint -- I. Introduction -- II. Potential Energy Functions for Liquid Water -- A. Heuristic Models -- B. Multisite Models -- 1. Three-Site Models -- 2. Four-Site Models -- 3. Five-Site Models -- 4. Six Sites and Beyond -- C. Molecular Multipole Models -- 1. The Multipole Expansion -- 2. The Approximate Multipole Expansion -- D. Atomic Multipole Models -- E. Summary -- III. Multipoles -- IV. The Water Molecule in the Pure Liquid -- A. Nuclear Geometry -- B. Electron Density -- C. Multipole Moments -- D. Electrostatic Potential -- E. Summary -- V. Liquid Water -- A. Structure -- B. Density -- C. Thermodynamics -- D. Dynamics -- E. Dielectric Properties -- F. Summary -- VI. Aqueous Solutions -- A. Ionic Solvation -- B. Hydrophobic Solvation -- VII. Conclusions -- References -- Construction of Energy Functions for Lattice Heteropolymer Models: Efficient Encodings for Constraint Satisfaction Programming and Quantum Annealing -- I. Introduction -- A. Motivation and Background -- B. Overview of Mapping Procedure -- II. The ''Turn'' Encoding of Self-Avoiding Walks -- A. Embedding Physical Structure -- B. ''Turn Ancilla'' Construction of E(q) -- 1. Construction of Eback (q) -- 2. Construction of Eoverlap (q) with Ancilla Variables -- 3. Construction of Epair (q) with Ancilla Variables
C. ''Turn Circuit'' Construction of E(q) -- 1. Sum Strings -- 2. Construction of Eoverlap (q) with Circuit -- 3. Construction of Epair (q) with Circuit -- III. The ''Diamond'' Encoding of SAWs -- A. Embedding Physical Structure -- B. Natively 2-Local E(q) -- 1. Construction of Eone (q) -- 2. Construction of Econnect (q) -- 3. Construction of Eoverlap (q) -- 4. Construction of Epair (q) -- IV. Pseudo-Boolean Function to W-SAT -- A. MAX-SAT and W-SAT -- B. Constructing WCNF Clauses -- C. Solving SAT Problems -- V. W-SAT to Integer--Linear Programming -- A. Mapping to ILP -- B. Solving ILP Problems -- VI. Locality Reductions -- VII. Quantum Realization -- A. Previous Experimental Implementation -- B. Six-Unit Miyazawa--Jernigan Protein -- 1.Eback (q) for Six-Unit SAW on 2D Lattice -- 2.Eoverlap(q) for Six-Unit SAW on 2D Lattice -- 3 Epair (q) for MJ Model PSVKMA -- 4. Setting λ Penalty Values -- 5. Reduction to 2-Local -- 6. QUBO Matrix and Solutions -- VIII. Conclusions -- References -- Author Index -- Subject Index
The cutting edge of research in chemical physics Each volume of the Advances in Chemical Physics series discusses aspects of the state of diverse subjects in chemical physics and related fields, with chapters written by top researchers in the field. Reviews published in Advances in Chemical Physics are typically longer than those published in journals, providing the space needed for readers to fully grasp the topic, including fundamentals, latest discoveries, applications, and emerging avenues of research. Volume 155 explores: Modeling viral capsid assembly Charges at aqueous interfaces, including the development of computational approaches in direct contact with the experiment Theory and simulation advances in solute precipitate nucleation A computational viewpoint of water in the liquid state Construction of energy functions for lattice heteropolymer models, including efficient encodings for constraint satisfaction programming and quantum annealing Advances in Chemical Physics is ideal for introducing novices to topics in chemical physics and serves as the perfect supplement to any advanced graduate class devoted to its study. The series also provides the foundation needed for more experienced researchers to advance research studies
Description based on publisher supplied metadata and other sources
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2020. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
Link Print version: Rice, Stuart A. Advances in Chemical Physics Somerset : John Wiley & Sons, Incorporated,c2014 9781118755778
Subject Chemical kinetics.;Chemistry, Physical and theoretical.;Molecular dynamics
Electronic books
Alt Author Dinner, Aaron R
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